1. Fac. of Agriculture, Assiut Univ.
Primer Design
Ameer Effat M. Elfarash
Dept. of Genetics
Fac. of Agriculture, Assiut Univ.

2. Why Are Primers Important?
Primers are what gives PCR its SPECIFICITY!!!
Good primer design: PCR works great.
Bad primer design: PCR works terrible.

3. PCR buffer
dNTP Mix
Taq DNA polymerase
Primers
Template
DDW
PCR Reagents

4. What is a primer?
A primer is a short synthetic oligonucleotide which is used in many molecular techniques from PCR to DNA sequencing.  These primers are designed to have a sequence which is the reverse complement of a region of template or target DNA to which we wish the primer to anneal. 

5. Very-Brief PCR Reminder
PCR is a method to amplify large quantities of a DNA covering a specific sequence.

6. Good Primer’s Characteristic
Primer length
5..TCAACTTAGCATGATCGGGTAGTAGCTTGACTGTACAACTCAGCAA..3’
18-24 bp for general applications

7. Too short---less specific Too long---wasting money
General rules for primer design
Primer length determines the specificity and significantly affect its annealing to the template
Too short -- low specificity, resulting in non-specific amplification
Too long -- decrease the template-binding efficiency at normal annealing temperature due to the higher probability of forming secondary structures such as hairpins.
Too short---less specific
Too long---wasting money

8. Base Composition 5 GTGGATGTGGTGTCGATGGC 3 5’ 3’
Usually, average (G+C) content around 50-60% will give us the right melting/annealing temperature for ordinary PCR reactions, and will give appropriate hybridization stability.
5 GTGGATGTGGTGTCGATGGC 3 5’ 3’

9. Max 3’end stability It’s critical that the stability at 3’ end be high
5 GTGGATGTGGTGTCGATGGC 3 5’

10. Melting Tm between 50-70 C are preferred
Primer melting temperature (Tm):
The melting temperature (Tm) is the most important factor in determining the optimal PCR annealing temperature (Ta).
Melting Tm between C are preferred

11. Tm Calculation Wallace rule: Bolton and McCarthy:
Tm = 4 * (G + C) + 2 * (A + T)
Bolton and McCarthy:
Tm = * Log [I] * (%GC) – 600/L
The nearest neighbor method (Santalucia et.al, 1998):

13. Annealing temperatures
37 – 60oC gradient

14. Primer Pair Matching
Primers work in pairs – forward primer and reverse primer. Since they are used in the same PCR reaction, it shall be ensured that the PCR condition is suitable for both of them.
One critical feature is their annealing temperatures, which shall be compatible with each other. The maximum difference allowed is 3 C. The closer their Tanneal are, the better.
5 CTGATCAAGTCGATGGCTTG 3 Fw
59 C
5 GATGGAGAGGCTTGACTGC 3 Rv
58 C

16. Determine the start and end sites of the DNA fragment you want to clone.
3`GACTAAGGACAGTTGCACAGTTACC..CTCAGGACTTCAGGAACGTAGCAC5`
5`CTGATTCCTGTCAACGTGTCAATGG..GAGTCCTGAAGTCCTTGCATCGTG3`
Choose the first bases in the 5` ends as forward and reverse primers.
3`GACTAAGGACAGTTGCACAGTTACC..CTCAGGACTTCAGGAACGTAGCAC5`
5`CTGATTCCTGTCAACGT3`----
Forward primer
Reverse primer
-----3`CTTCAGGAACGTAGCAC5`
5`CTGATTCCTGTCAACGTGTCAATGG..GAGTCCTGAAGTCCTTGCATCGTG3`

17. Avoid
A. Avoid hairpin and stem-loop formation

18. Avoid complementary at 3` end of primers

19. when is a “primer” a primer?5’ 3’ 5’ 3’ 5’ 3’ 3’ 5’

20. … PCR primers are designed to: For Cloning a special sequence
Full length
Gene of interest
Mutation Detection
Allelic discrimination
Gene expression ( mRNA)
Microbial agents detection
Quantification …
Disease
For Detection bp
Random ??

21. Random primers Example: RAPD-PCR RAPD = Random Amplified Polymorphic DNA
5`-TCG GCG GTT C-3`

23. Universal Primers Primers can be designed to amplify only one product.
Primers can also be designed to amplify multiple products. We call such primers “universal primers”. For example, design primers to amplify all HPV genes.
Strategy:
Align groups of sequences you want to amplify.
Find the most conservative regions at 5’ end and at 3’ end.
Design forward primer at the 5’ conservative region.
Design reverse primer at the 3’ conservative regions.
Matching forward and reverse primers to find the best pair.
Ensure uniqueness in all template sequences.
Ensure uniqueness in possible contaminant sources.

25. Cloning Overview Insert (your gene) + Functional Plasmid construct
Four main steps in cloning:
Insert synthesis
Restriction enzyme digest
Ligation
Transformation
Insert
(your gene) +
Functional
construct
Plasmid
(vector)

26. 5’ 3’
PCR RE

27. Ligation of the Insert into the Vector+
Ligation covalently attaches the vector and the insert via a phosphodiester bond (5’phosphate and 3’ hydroxyl of the next base)

28. Restriction enzymes (NEB)
oligo % cleavage
sequence 2h 20h
BamHI CGGATCCG
CGGGATCCCG >90 >90
CGCGGATCCGCG >90 >90
EcoRI GGAATTCC >90 >90
CGGAATTCCG >90 >90
CCGGAATTCCGG >90 >90
HindIII CAAGCTTG
CCAAGCTTGG
CCCAAGCTTGGG
NcoI CCCATGGG
CATGCCATGGCATG
NdeI GGGTTTCATATGAAACCC
GGAATTCCATATGGAATTCC >90

30. Site-directed mutagenesis

32. Web-based Softwares

33. Installable Softwares

34. Primer3

37. Primer3 Output